Retroviral integrase superfamily: the structural perspective

Nowotny, Marcin

doi:10.1038/embor.2008.256

Cited by 171 publications

(200 citation statements)

References 50 publications

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“…Conservation and Specialization of Viral Headful NucleasesThe 2.02 Å crystal structure of P22 L-terminase nuclease domain reveals the detailed architecture of a headful nuclease, related in fold and catalytic mechanism to the RNase H1 family of retroviral integrase superfamily (45). Despite minimal sequence identity (below 16%), P22 nuclease domain is remarkably similar to those previously observed in SPP1 (18), T4 (6), and HHV-5 (19).…”

Section: Discussionsupporting

confidence: 48%

Structure of P22 Headful Packaging Nuclease

Roy

Cingolani

2012

Journal of Biological Chemistry

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Background:The headful nuclease is essential for genome processing during viral DNA packaging. Results: The crystal structure of P22 nuclease reveals a seven-stranded ␤-sheet core with two magnesium ions poised for catalysis. Conclusion: P22 headful nuclease is active only in the context of the large terminase. Significance: The C-terminal headful nuclease is activated by intramolecular cross-talk with the N-terminal ATPase domain.

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Section: Discussionsupporting

confidence: 48%

Structure of P22 Headful Packaging Nuclease

Roy

Cingolani

2012

Journal of Biological Chemistry

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“…S5) (15)(16)(17). Incubation with Mg 2+ generated a radiolabeled 120-nt product that comigrated with the bottom strand cleavage product of NcoI, demonstrating that TnpA introduces specific nicks at the transposon 3′ ends as predicted from current models of copy-in replicative transposition ( Fig.…”

Section: Resultsmentioning

confidence: 98%

“…4B, compare lanes 8-13 with lanes [14][15][16][17][18][19]. Thus, an OH nucleophile at the primary 3′ end cleavage site is not a prerequisite for cleaving the opposite DNA strand.…”

Section: Resultsmentioning

confidence: 99%

“…The active site is included in an RNaseH fold structural domain that is characteristic of a variety of polynucleotide hydrolases and transferases ( Fig. 1A) (16,17). In addition to mediating transposition, TnpA is responsible for target immunity, a long-range regulatory phenomenon whereby transposons avoid inserting more than once into the same DNA region (18,19).…”

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confidence: 99%

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Unlocking Tn3-family transposase activity in vitro unveils an asymetric pathway for transposome assembly

Nicolas

Oger

Nguyen

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The Tn3 family is a widespread group of replicative transposons that are notorious for their contribution to the dissemination of antibiotic resistance and the emergence of multiresistant pathogens worldwide. The TnpA transposase of these elements catalyzes DNA breakage and rejoining reactions required for transposition. It also is responsible for target immunity, a phenomenon that prevents multiple insertions of the transposon into the same genomic region. However, the molecular mechanisms whereby TnpA acts in both processes remain unknown. Here, we have developed sensitive biochemical assays for the TnpA transposase of the Tn3-family transposon Tn4430 and used these assays to characterize previously isolated TnpA mutants that are selectively affected in immunity. Compared with wild-type TnpA, these mutants exhibit deregulated activities. They spontaneously assemble a unique asymmetric synaptic complex in which one TnpA molecule simultaneously binds two transposon ends. In this complex, TnpA is in an activated state competent for DNA cleavage and strand transfer. Wild-type TnpA can form this complex only on precleaved ends mimicking the initial step of transposition. The data suggest that transposition is controlled at an early stage of transpososome assembly, before DNA cleavage, and that mutations affecting immunity have unlocked TnpA by stabilizing the protein in a monomeric activated synaptic configuration. We propose an asymmetric pathway for coupling active transpososome assembly with proper target recruitment and discuss this model with respect to possible immunity mechanisms.

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“…Retroviral INs belong to a superfamily of proteins known as the retroviral IN superfamily, which contains other nucleic acid-metabolizing enzymes such as RNase H, RuvC, bacteriophage MuA transposase, and the nuclease component of the RNA-induced silencing complex Argonaute (9). Common features of these enzymes are the RNase H fold adopted by their catalytic domains and active sites composed of electronegative Asp and Glu side chains (9, 10).…”

Section: In Domain Structure and Reaction Mechanismmentioning

confidence: 99%

Retroviral Integrase Proteins and HIV-1 DNA Integration

Krishnan

Engelman

2012

Journal of Biological Chemistry

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Retroviral integrases catalyze two reactions, 3-processing of viral DNA ends, followed by integration of the processed ends into chromosomal DNA. X-ray crystal structures of integrase-DNA complexes from prototype foamy virus, a member of the Spumavirus genus of Retroviridae, have revealed the structural basis of integration and how clinically relevant integrase strand transfer inhibitors work. Underscoring the translational potential of targeting virus-host interactions, small molecules that bind at the host factor lens epithelium-derived growth factor/ p75-binding site on HIV-1 integrase promote dimerization and inhibit integrase-viral DNA assembly and catalysis. Here, we review recent advances in our knowledge of HIV-1 DNA integration, as well as future research directions.Retroviral replication proceeds through an obligate proviral or integrated DNA recombination intermediate. Integration provides a favorable environment for efficient gene expression, ensures inheritance of the virus in both daughter cells during mitosis, and forms the basis for latent HIV-1 reservoirs that persist in the face of highly active antiretroviral therapy. The early events of retroviral replication take place within the context of nucleoprotein complexes that are derived from the core of the infecting virus particle (1, 2). Within the confines of the reverse transcription complex (RTC), 2 the reverse transcriptase enzyme copies single-stranded viral RNA into a linear double-stranded DNA molecule containing a copy of the LTR sequence at each end. The viral integrase (IN) engages the LTR ends prior to catalyzing two spatially and temporally distinct chemical reactions. Soon after their synthesis (3), IN site-specifically processes each LTR end adjacent to an invariant CA dinucleotide (4, 5), yielding CA OH 3Ј-hydroxyl groups that serve as the nucleophiles for the second reaction, DNA strand transfer. Because the viral replication intermediate at this point gains the ability to catalyze DNA strand transfer activity, 3Ј-processing operationally marks the transition of the RTC to the pre-integration complex (PIC) (Fig. 1). In the strand transfer step, IN utilizes the 3Ј-oxygen atoms to cut chromosomal DNA in a staggered fashion and simultaneously join the viral DNA ends to the 5Ј-phosphates of the target DNA (4, 6, 7). The resulting DNA recombination intermediate, with unjoined viral DNA 5Ј-ends, is repaired by host cell enzymes to yield the integrated provirus flanked by the duplication of the sequence of the staggered DNA cut (Fig. 1). The spumaviruses, which compose one of seven Retroviridae genera, are an exception to this generalized scheme, as DNA synthesis is largely complete prior to target cell infection (8). Research on the functionality of the active nucleoprotein complexes that mediate HIV-1 DNA integration has led to the development of antiviral inhibitors that target the IN and block integration. IN Domain Structure and Reaction MechanismRetroviral INs belong to a superfamily of proteins known as the retroviral IN superfam...

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Retroviral integrase superfamily: the structural perspective

Cited by 171 publications

References 50 publications

Structure of P22 Headful Packaging Nuclease

Structure of P22 Headful Packaging Nuclease

Unlocking Tn3-family transposase activity in vitro unveils an asymetric pathway for transposome assembly

Retroviral Integrase Proteins and HIV-1 DNA Integration

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